Thank you Catarina and Peter! This will help me very much. So, I manually phosphorylated my serine using the pymol plugin PyTM's. Then I manually modified the name of my serine from SER to S2P in the pdb file and tried to compute the topology via AMBER-ILDN. As expected, it didn't work. So I started adding the S2P residue, as Peter reported. However, I'm having some troubles in interpreting the database. I got the charges correctly (they sum to -2 so I suppose they are correct) but I cannot find the bonds, dihedrals and impropers which are required in the aminoacids.rtp file. Do you know how can I do?
Thank you again! Your support is priceless. Simone Il giorno dom 10 gen 2016 alle ore 13:09 Catarina A. Carvalheda dos Santos < c.a.c.dossan...@dundee.ac.uk> ha scritto: > Yes, Peter is right. > > I was assuming the residue S2P is already in the amber force field. If not, > you can use the phosphoserine parameters derived by Homeyer and co-workers > <http://rd.springer.com/article/10.1007%2Fs00894-005-0028-4> and > distributed in the AMBER parameter database > <http://sites.pharmacy.manchester.ac.uk/bryce/amber/>, and follow Peter's > suggestions. > > Cheers, > > On 10 January 2016 at 10:13, Peter Stern <peter.st...@weizmann.ac.il> > wrote: > > > The instructions for adding a new residue are here: > > > > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=add+new+residue > > > > If you cannot understand these instructions, then most probably you will > > have to read about them in Chapter 5 of the gromacs manual in order to > > understand what all the different files mentioned are about. In > > particular, you will have to define a new residue, e.g. SERP or something > > like that in the residuetypes.dat file, but also in the aminoacids.rtp > > file making sure that all the new bonds, angles and dihedrals are defined > > and that these also exist in the ffbonded.itp file. The biggest > challenge > > will be assigning the correct charges to the atoms of the new residue so > > that the net charge is now, for example, -1. One way to do this is to > run > > Gaussian. You need to google this a bit. > > > > Regards, > > Peter > > > > -----Original Message----- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Simone > > Bolognini > > Sent: Sunday, January 10, 2016 11:08 AM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Serine phosphorylation > > > > Thank you for your support, but I find the instructions on the website > > extremely unclear to me. There are some commands to be run which are nor > > gromacs neither bash commands that pretty puzzle me. However, I'd better > be > > more specific in explaining my problem: I have a protein whose pdb > contains > > a particular serine in which I am interested on. Now, for some reasons, I > > need to change this serine (and only this one!) to a phosphorylated one > and > > run some MD production using AMBER-ILDN with this new configuration. What > > should I do exactly? Can you provide me a sequence of steps which I > should > > follow in order to go from the starting pdb to the actual simulation? > > > > As always, thank you very much for your help! > > Simone > > > > Il giorno ven 8 gen 2016 alle ore 13:30 Changrong Ge < > > changrong...@gmail.com> ha scritto: > > > > > http://selene.princeton.edu/FFPTM/ > > > > > > On Fri, Jan 8, 2016 at 9:52 AM, Simone Bolognini > > > <simo.bologn...@gmail.com > > > > > > > wrote: > > > > > > > Hi everyone, > > > > I need to run some MD simulations with a protein where a particular > > > serine > > > > should be phosphorylated. Since in the original pdb the serine is > > > actually > > > > not, I guess I should modify something 'by hand'. I'm going to use > > > > AMBER-ILDN ff. Can anyone of you tell me what should I do? My first > > > > guess was to generate the topology and then directly substitute my > > > > serine with the phosphorylated one (looking for the AMBER-ILDN > > > > parameters), but sincerely I don't know if this is the correct way to > > proceed. > > > > > > > > Thanks a lot for your support! > > > > Simone > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > or send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > -- > > > > > > Changrong Ge, PhD > > > > > > Division of Medical Inflammation Research Department of Medical > > > Biochemistry and Biophysics (MBB) Karolinska Institutet Scheeles väg > > > 2, B2 Plan 4 > > > SE-171 77 Stockholm > > > Sweden > > > Tel: +46-8-524 86337 , Mobile: +46-(0)76-2878 029 > > > Fax: +46-8-524 87750 , Email: changrong...@ki.se > > > <changr...@dbb.su.se> or changrong...@gmail.com > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > > > > > -- > Catarina A. Carvalheda > > PhD Student > Computational Biology Division > SSE & SLS > University of Dundee > DD1 5EH, Dundee, Scotland, UK > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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